David,
I did some research and sometimes there are CAD objects that aren't friendly to deleting, which I thing requires a purge command. Apparently there is a certain Windchill installation where you install it local to your machine that gives you functions such as purge. As the Windchill allocated for FIRST, is cloud only, I don't think the functions such as purge are available. What ended up working for me is I went to the highest level directory and applied "delete" and it finally wiped it out that directory and everything below it. Nothing left!
Just for grins I have tried uploading all the CAD files of "How to Model almost Anything" by iself, and it gives a whole bunch of errors, and skips but does not give details on what is tripping up the upload. Local to Creo I open the Glider and has a missing canopy. I open the Lego Truck and it appears and disappers and then shows the tail of an airplane. Its a total "head trip" LOL. It is kind of funny and curious how it just starts linking unrelated things or just skips over them.
My conclusion is that loading up files to Windchill is not for the faint hearted, and is not a seamless or even predictable effort. I think there might be some dependency preprocessor that munches on these CAD objects and sometimes it might make wild haired assumptions as it tries to load things up and figure out depedencies. Seeing a truck that morphed into a plane tail section was rather funny and amusing.
I looked at a couple relationships before uploading that had absolutely no reference to some file names that appeaed later during the upload process. I think Creo-Windchil l generated these filenames that weren't part of the original naming scheme which resulted in a couple of ghost files.
My conclusion so far is that Windchill is primarily intended for strict revisioning of an ongoing project where perhaps a dedicated Windchill administrator might have to intervene at times to make these objects congruent with Windchill. Trying to get end users to push their own CAD practice files, tutorials, etc. would only be a recipe for disaster with this environment. My fear is that sometimes squirly behavior might require PTC involvment and diagnostics. Its a complex system. I bet its great for revisioning a truck, an automobile, etc for large scale complex products though.